Starting phenix.real_space_refine
on Tue Mar  3 18:21:45 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662_neut_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2026/7df8_30662.map"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    4915      2.51       5
     N    1171      2.21       5
     O    1378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7505
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 918, 7148
          Classifications: {'peptide': 918}
          Link IDs: {'PTRANS': 46, 'TRANS': 871}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "K"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "R"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 245
          Unusual residues: {'CLR': 4, 'LMT': 1, 'NAG': 7}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
  Time building chain proxies: 1.63, per 1000 atoms: 0.22
  Number of scatterers: 7505
  At special positions: 0
  Unit cell: (94.429, 77.453, 131.564, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1378      8.00
     N    1171      7.00
     C    4915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 525 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 920 " - pdb=" SG  CYS A 925 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS A 993 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 980 " - pdb=" SG  CYS A 989 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG H   1 " - " NAG H   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG K   2 " - " NAG K   3 "
      " NAG R   1 " - " NAG R   2 "
      " NAG R   2 " - " NAG R   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 431 "
      " NAG A1302 " - " ASN A 464 "
      " NAG A1303 " - " ASN A 506 "
      " NAG A1304 " - " ASN A 416 "
      " NAG A1305 " - " ASN A 479 "
      " NAG A1306 " - " ASN A 927 "
      " NAG A1307 " - " ASN A1075 "
      " NAG H   1 " - " ASN A 497 "
      " NAG K   1 " - " ASN A 909 "
      " NAG R   1 " - " ASN A1037 "
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 184.1 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      58.5% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 332 through 350
      removed outlier: 3.736A  pdb=" N   LEU A 337 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 350 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 368
      removed outlier: 3.697A  pdb=" N   ILE A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 369 through 371
      No H-bonds generated for 'chain 'A' and resid 369 through 371'
    Processing helix  chain 'A' and resid 388 through 402
    Processing helix  chain 'A' and resid 437 through 453
      removed outlier: 4.076A  pdb=" N   GLU A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 471
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.659A  pdb=" N   TYR A 493 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 502
    Processing helix  chain 'A' and resid 517 through 528
      removed outlier: 3.692A  pdb=" N   HIS A 521 " --> pdb=" O   ASP A 517 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 567
      removed outlier: 3.516A  pdb=" N   GLU A 566 " --> pdb=" O   ASP A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 607
      removed outlier: 4.349A  pdb=" N   ALA A 587 " --> pdb=" O   ASP A 583 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 594 " --> pdb=" O   LYS A 590 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 626
      removed outlier: 3.626A  pdb=" N   ILE A 625 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASN A 626 " --> pdb=" O   GLU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
      removed outlier: 3.863A  pdb=" N   LEU A 633 " --> pdb=" O   THR A 629 " (cutoff:3.500A)
      Proline residue:  A 634  - end of helix
    Processing helix  chain 'A' and resid 637 through 647
      removed outlier: 3.933A  pdb=" N   ILE A 641 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 690
      removed outlier: 3.543A  pdb=" N   GLY A 669 " --> pdb=" O   LYS A 665 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A 679 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   PHE A 687 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER A 688 " --> pdb=" O   MET A 684 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A 689 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 690 " --> pdb=" O   PHE A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 3.733A  pdb=" N   VAL A 702 " --> pdb=" O   ILE A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 724
      removed outlier: 3.563A  pdb=" N   PHE A 715 " --> pdb=" O   ALA A 711 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 716 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 720 " --> pdb=" O   ILE A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 743 through 761
    Processing helix  chain 'A' and resid 762 through 764
      No H-bonds generated for 'chain 'A' and resid 762 through 764'
    Processing helix  chain 'A' and resid 766 through 790
      removed outlier: 3.530A  pdb=" N   THR A 771 " --> pdb=" O   PRO A 767 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   PHE A 772 " --> pdb=" O   ALA A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 802
      removed outlier: 3.557A  pdb=" N   ARG A 801 " --> pdb=" O   LEU A 797 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN A 802 " --> pdb=" O   ASP A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 836 through 841
    Processing helix  chain 'A' and resid 844 through 864
      removed outlier: 4.305A  pdb=" N   LEU A 850 " --> pdb=" O   ARG A 846 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU A 854 " --> pdb=" O   LEU A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 872 through 877
      removed outlier: 3.603A  pdb=" N   ALA A 876 " --> pdb=" O   GLN A 873 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 877 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 894
      removed outlier: 3.637A  pdb=" N   TYR A 886 " --> pdb=" O   TYR A 882 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE A 894 " --> pdb=" O   LEU A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 918
      removed outlier: 3.768A  pdb=" N   ALA A 918 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 938
      removed outlier: 3.620A  pdb=" N   THR A 938 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 961
    Processing helix  chain 'A' and resid 1004 through 1016
      removed outlier: 3.549A  pdb=" N   LEU A1012 " --> pdb=" O   PHE A1008 " (cutoff:3.500A)
      Proline residue:  A1013  - end of helix
    Processing helix  chain 'A' and resid 1058 through 1081
      removed outlier: 3.827A  pdb=" N   TYR A1062 " --> pdb=" O   ASN A1058 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR A1063 " --> pdb=" O   SER A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1103
      removed outlier: 4.055A  pdb=" N   TYR A1102 " --> pdb=" O   THR A1098 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1106
      No H-bonds generated for 'chain 'A' and resid 1104 through 1106'
    Processing helix  chain 'A' and resid 1107 through 1118
      removed outlier: 3.794A  pdb=" N   GLU A1111 " --> pdb=" O   THR A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1125
    Processing helix  chain 'A' and resid 1126 through 1131
    Processing helix  chain 'A' and resid 1140 through 1160
    Processing helix  chain 'A' and resid 1164 through 1176
      removed outlier: 3.598A  pdb=" N   ILE A1169 " --> pdb=" O   ALA A1165 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASN A1170 " --> pdb=" O   VAL A1166 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY A1176 " --> pdb=" O   VAL A1172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1191
      removed outlier: 3.830A  pdb=" N   PHE A1181 " --> pdb=" O   MET A1177 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   HIS A1184 " --> pdb=" O   GLU A1180 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ILE A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1196 through 1216
      removed outlier: 3.505A  pdb=" N   MET A1208 " --> pdb=" O   ALA A1204 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   SER A1210 " --> pdb=" O   ILE A1206 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ALA A1211 " --> pdb=" O   SER A1207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1226
    Processing helix  chain 'A' and resid 1227 through 1229
      No H-bonds generated for 'chain 'A' and resid 1227 through 1229'
    Processing helix  chain 'A' and resid 1232 through 1239
    Processing helix  chain 'A' and resid 1240 through 1255
      removed outlier: 3.513A  pdb=" N   LEU A1249 " --> pdb=" O   LEU A1245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1266
      removed outlier: 3.977A  pdb=" N   TYR A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423
    Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458
      removed outlier: 4.119A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 508
    Processing sheet with id=AA6, first strand: chain 'A' and resid 946 through 951
      removed outlier: 6.707A  pdb=" N   TYR A1052 " --> pdb=" O   ALA A 947 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   MET A1050 " --> pdb=" O   PRO A 949 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038
      removed outlier: 3.914A  pdb=" N   ALA A1046 " --> pdb=" O   ASN A1037 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    969 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.79 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2172
        1.34 -     1.46: 1551
        1.46 -     1.58: 3907
        1.58 -     1.70: 0
        1.70 -     1.82: 64
  Bond restraints: 7694
  Sorted by residual:
  bond pdb=" C   ASP A 378 "
       pdb=" N   PRO A 379 "
    ideal  model  delta    sigma   weight residual
    1.334  1.401 -0.067 2.34e-02 1.83e+03 8.11e+00
  bond pdb=" C3' LMT A1308 "
       pdb=" O3' LMT A1308 "
    ideal  model  delta    sigma   weight residual
    1.404  1.350  0.054 2.00e-02 2.50e+03 7.35e+00
  bond pdb=" C6' LMT A1308 "
       pdb=" O6' LMT A1308 "
    ideal  model  delta    sigma   weight residual
    1.407  1.356  0.051 2.00e-02 2.50e+03 6.43e+00
  bond pdb=" C2B LMT A1308 "
       pdb=" O2B LMT A1308 "
    ideal  model  delta    sigma   weight residual
    1.410  1.362  0.048 2.00e-02 2.50e+03 5.72e+00
  bond pdb=" C3B LMT A1308 "
       pdb=" O3B LMT A1308 "
    ideal  model  delta    sigma   weight residual
    1.406  1.358  0.048 2.00e-02 2.50e+03 5.67e+00
  ... (remaining 7689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 10139
        2.24 -     4.48: 306
        4.48 -     6.72: 41
        6.72 -     8.97: 10
        8.97 -    11.21: 2
  Bond angle restraints: 10498
  Sorted by residual:
  angle pdb=" N   ASP A 378 "
        pdb=" CA  ASP A 378 "
        pdb=" C   ASP A 378 "
      ideal   model   delta    sigma   weight residual
     109.81  121.02  -11.21 2.21e+00 2.05e-01 2.57e+01
  angle pdb=" N   VAL A 371 "
        pdb=" CA  VAL A 371 "
        pdb=" C   VAL A 371 "
      ideal   model   delta    sigma   weight residual
     113.53  109.42    4.11 9.80e-01 1.04e+00 1.76e+01
  angle pdb=" CA  ASP A 378 "
        pdb=" C   ASP A 378 "
        pdb=" N   PRO A 379 "
      ideal   model   delta    sigma   weight residual
     118.44  124.68   -6.24 1.59e+00 3.96e-01 1.54e+01
  angle pdb=" N   ALA A 744 "
        pdb=" CA  ALA A 744 "
        pdb=" C   ALA A 744 "
      ideal   model   delta    sigma   weight residual
     109.81  117.67   -7.86 2.21e+00 2.05e-01 1.26e+01
  angle pdb=" N   ARG A 801 "
        pdb=" CA  ARG A 801 "
        pdb=" C   ARG A 801 "
      ideal   model   delta    sigma   weight residual
     111.33  115.62   -4.29 1.21e+00 6.83e-01 1.26e+01
  ... (remaining 10493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.77: 4653
       22.77 -    45.55: 275
       45.55 -    68.32: 23
       68.32 -    91.09: 14
       91.09 -   113.87: 5
  Dihedral angle restraints: 4970
    sinusoidal: 2299
      harmonic: 2671
  Sorted by residual:
  dihedral pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.34   70.34     1      1.00e+01 1.00e-02 6.37e+01
  dihedral pdb=" CB  CYS A 920 "
           pdb=" SG  CYS A 920 "
           pdb=" SG  CYS A 925 "
           pdb=" CB  CYS A 925 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.37   39.37     1      1.00e+01 1.00e-02 2.18e+01
  dihedral pdb=" CA  GLU A 381 "
           pdb=" C   GLU A 381 "
           pdb=" N   LEU A 382 "
           pdb=" CA  LEU A 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.61   20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 4967 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1035
       0.061 -    0.122: 197
       0.122 -    0.183: 23
       0.183 -    0.244: 12
       0.244 -    0.305: 7
  Chirality restraints: 1274
  Sorted by residual:
  chirality pdb=" CA  ASP A 378 "
            pdb=" N   ASP A 378 "
            pdb=" C   ASP A 378 "
            pdb=" CB  ASP A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" C13 CLR A1312 "
            pdb=" C12 CLR A1312 "
            pdb=" C14 CLR A1312 "
            pdb=" C17 CLR A1312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.63   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  THR A 377 "
            pdb=" CA  THR A 377 "
            pdb=" OG1 THR A 377 "
            pdb=" CG2 THR A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 1271 not shown)

  Planarity restraints: 1282
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG K   3 "   -0.336 2.00e-02 2.50e+03   2.91e-01 1.06e+03
        pdb=" C7  NAG K   3 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG K   3 "   -0.047 2.00e-02 2.50e+03
        pdb=" N2  NAG K   3 "    0.511 2.00e-02 2.50e+03
        pdb=" O7  NAG K   3 "   -0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1306 "   -0.329 2.00e-02 2.50e+03   2.86e-01 1.02e+03
        pdb=" C7  NAG A1306 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG A1306 "   -0.057 2.00e-02 2.50e+03
        pdb=" N2  NAG A1306 "    0.505 2.00e-02 2.50e+03
        pdb=" O7  NAG A1306 "   -0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG K   1 "   -0.292 2.00e-02 2.50e+03   2.45e-01 7.52e+02
        pdb=" C7  NAG K   1 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG K   1 "   -0.187 2.00e-02 2.50e+03
        pdb=" N2  NAG K   1 "    0.418 2.00e-02 2.50e+03
        pdb=" O7  NAG K   1 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1279 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 41
        2.57 -     3.15: 5990
        3.15 -     3.73: 11000
        3.73 -     4.32: 15457
        4.32 -     4.90: 26240
  Nonbonded interactions: 58728
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 801 "
            pdb=" OE1 GLN A 802 "
     model   vdw
     1.986 3.120
  nonbonded pdb=" OG1 THR A1039 "
            pdb=" OD1 ASP A1041 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OE1 GLU A 624 "
            pdb=" OG  SER A 881 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OG  SER A1192 "
            pdb=" OE1 GLU A1203 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG1 THR A 407 "
            pdb=" O6B LMT A1308 "
     model   vdw
     2.248 3.040
  ... (remaining 58723 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'K'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.240
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   7714  Z= 0.283
  Angle     :  0.914  14.373  10553  Z= 0.443
  Chirality :  0.056   0.305   1274
  Planarity :  0.017   0.291   1272
  Dihedral  : 14.527 113.869   3233
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.13 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.20), residues: 912
  helix: -2.75 (0.15), residues: 496
  sheet: -1.24 (0.56), residues: 78
  loop : -2.63 (0.27), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.012   0.001   TYR A 546 
 PHE   0.037   0.002   PHE A 832 
 TRP   0.011   0.002   TRP A 953 
 HIS   0.013   0.002   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 7694)
  covalent geometry    : angle       0.88009 (10498)
  SS BOND              : bond        0.00248 (    5)
  SS BOND              : angle       2.73473 (   10)
  hydrogen bonds       : bond        0.22560 (  329)
  hydrogen bonds       : angle       7.71946 (  969)
  link_BETA1-4         : bond        0.00415 (    5)
  link_BETA1-4         : angle       1.20722 (   15)
  link_NAG-ASN         : bond        0.00694 (   10)
  link_NAG-ASN         : angle       4.44123 (   30)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  425 LEU cc_start: 0.8743 (tp) cc_final: 0.8506 (tp)
REVERT: A  517 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0)
REVERT: A  543 MET cc_start: 0.7947 (mtp) cc_final: 0.7619 (mtm)
REVERT: A  705 LEU cc_start: 0.8308 (tt) cc_final: 0.7661 (mp)
REVERT: A  727 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.7081 (mpt-90)
REVERT: A  742 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8491 (ttm-80)
REVERT: A  788 MET cc_start: 0.8361 (tpp) cc_final: 0.8138 (tpp)
REVERT: A  798 ASP cc_start: 0.8176 (t70) cc_final: 0.7897 (t0)
REVERT: A  955 ASP cc_start: 0.7881 (t0) cc_final: 0.7637 (t0)
REVERT: A  970 TYR cc_start: 0.8061 (m-80) cc_final: 0.7576 (m-80)
REVERT: A 1043 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6693 (tt0)
REVERT: A 1050 MET cc_start: 0.9153 (ttt) cc_final: 0.8849 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0902
  time to fit residues: 12.3208
Evaluate side-chains
  65 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.112194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.088024 restraints weight = 12013.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.65
r_work: 0.2916 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7714  Z= 0.143
  Angle     :  0.676  11.272  10553  Z= 0.310
  Chirality :  0.044   0.296   1274
  Planarity :  0.005   0.053   1272
  Dihedral  : 10.958 108.788   1621
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  5.39 %
    Favored  : 93.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.26), residues: 912
  helix: -0.52 (0.22), residues: 494
  sheet: -1.13 (0.55), residues: 84
  loop : -2.06 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 723 
 TYR   0.009   0.001   TYR A 546 
 PHE   0.022   0.001   PHE A 930 
 TRP   0.008   0.001   TRP A 960 
 HIS   0.007   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7694)
  covalent geometry    : angle       0.64017 (10498)
  SS BOND              : bond        0.00235 (    5)
  SS BOND              : angle       1.16644 (   10)
  hydrogen bonds       : bond        0.04713 (  329)
  hydrogen bonds       : angle       4.67370 (  969)
  link_BETA1-4         : bond        0.00534 (    5)
  link_BETA1-4         : angle       1.83327 (   15)
  link_NAG-ASN         : bond        0.00637 (   10)
  link_NAG-ASN         : angle       3.87965 (   30)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7555 (mt) cc_final: 0.7268 (mp)
REVERT: A  543 MET cc_start: 0.8574 (mtp) cc_final: 0.8335 (mtm)
REVERT: A  705 LEU cc_start: 0.8559 (tt) cc_final: 0.7900 (mt)
REVERT: A  727 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.7232 (mpt-90)
REVERT: A  766 MET cc_start: 0.8384 (mmm) cc_final: 0.7828 (mmt)
REVERT: A  955 ASP cc_start: 0.8565 (t0) cc_final: 0.8223 (t0)
REVERT: A  970 TYR cc_start: 0.8101 (m-80) cc_final: 0.7695 (m-80)
REVERT: A 1043 GLN cc_start: 0.7345 (tp-100) cc_final: 0.7105 (tt0)
REVERT: A 1252 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8407 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 82
  average time/residue: 0.0794
  time to fit residues: 9.2581
Evaluate side-chains
  72 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue 1252 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.110327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.086027 restraints weight = 11876.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.64
r_work: 0.2874 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7714  Z= 0.204
  Angle     :  0.676  10.242  10553  Z= 0.310
  Chirality :  0.044   0.252   1274
  Planarity :  0.004   0.038   1272
  Dihedral  : 10.259 107.123   1621
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.24 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.27), residues: 912
  helix:  0.14 (0.24), residues: 501
  sheet: -0.99 (0.54), residues: 84
  loop : -1.79 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 723 
 TYR   0.010   0.001   TYR A 546 
 PHE   0.023   0.002   PHE A 930 
 TRP   0.010   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 7694)
  covalent geometry    : angle       0.64515 (10498)
  SS BOND              : bond        0.00373 (    5)
  SS BOND              : angle       1.06157 (   10)
  hydrogen bonds       : bond        0.04565 (  329)
  hydrogen bonds       : angle       4.37956 (  969)
  link_BETA1-4         : bond        0.00682 (    5)
  link_BETA1-4         : angle       1.70964 (   15)
  link_NAG-ASN         : bond        0.00457 (   10)
  link_NAG-ASN         : angle       3.61834 (   30)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7535 (mt) cc_final: 0.7249 (mp)
REVERT: A  517 ASP cc_start: 0.8831 (t0) cc_final: 0.8578 (t0)
REVERT: A  543 MET cc_start: 0.8709 (mtp) cc_final: 0.8480 (mtm)
REVERT: A  705 LEU cc_start: 0.8624 (tt) cc_final: 0.7822 (mt)
REVERT: A  727 ARG cc_start: 0.7457 (mtt-85) cc_final: 0.7235 (mpt-90)
REVERT: A  851 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8519 (tt)
REVERT: A  955 ASP cc_start: 0.8595 (t0) cc_final: 0.8268 (t0)
REVERT: A  970 TYR cc_start: 0.8130 (m-80) cc_final: 0.7849 (m-80)
REVERT: A 1252 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8469 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0699
  time to fit residues: 8.0762
Evaluate side-chains
  73 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  789 SER
Chi-restraints excluded: chain A residue  851 LEU
Chi-restraints excluded: chain A residue 1252 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 59 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 334 HIS
A 515 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.088553 restraints weight = 11830.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.62
r_work: 0.2931 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7714  Z= 0.108
  Angle     :  0.598   9.530  10553  Z= 0.271
  Chirality :  0.041   0.266   1274
  Planarity :  0.003   0.032   1272
  Dihedral  :  9.543 105.944   1621
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.94 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.28), residues: 912
  helix:  0.62 (0.24), residues: 501
  sheet: -0.70 (0.57), residues: 84
  loop : -1.58 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 693 
 TYR   0.008   0.001   TYR A 886 
 PHE   0.013   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.006   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7694)
  covalent geometry    : angle       0.57194 (10498)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.70132 (   10)
  hydrogen bonds       : bond        0.03493 (  329)
  hydrogen bonds       : angle       4.14075 (  969)
  link_BETA1-4         : bond        0.00636 (    5)
  link_BETA1-4         : angle       1.58613 (   15)
  link_NAG-ASN         : bond        0.00543 (   10)
  link_NAG-ASN         : angle       3.12153 (   30)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7525 (mt) cc_final: 0.7251 (mp)
REVERT: A  517 ASP cc_start: 0.8651 (t0) cc_final: 0.8411 (t0)
REVERT: A  705 LEU cc_start: 0.8542 (tt) cc_final: 0.7795 (mt)
REVERT: A  955 ASP cc_start: 0.8532 (t0) cc_final: 0.8240 (t0)
REVERT: A  970 TYR cc_start: 0.8263 (m-80) cc_final: 0.7861 (m-80)
REVERT: A 1208 MET cc_start: 0.9156 (tpp) cc_final: 0.8945 (tpt)
REVERT: A 1252 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0729
  time to fit residues: 8.3257
Evaluate side-chains
  73 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  789 SER
Chi-restraints excluded: chain A residue  885 ASP
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1252 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.085541 restraints weight = 11767.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.58
r_work: 0.2877 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7714  Z= 0.205
  Angle     :  0.658   9.751  10553  Z= 0.302
  Chirality :  0.044   0.251   1274
  Planarity :  0.003   0.030   1272
  Dihedral  :  9.480 105.524   1621
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.58 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.28), residues: 912
  helix:  0.70 (0.24), residues: 501
  sheet: -0.80 (0.54), residues: 84
  loop : -1.48 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1241 
 TYR   0.010   0.001   TYR A 546 
 PHE   0.022   0.002   PHE A 930 
 TRP   0.010   0.001   TRP A 960 
 HIS   0.003   0.001   HIS A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 7694)
  covalent geometry    : angle       0.63095 (10498)
  SS BOND              : bond        0.00374 (    5)
  SS BOND              : angle       0.90760 (   10)
  hydrogen bonds       : bond        0.04236 (  329)
  hydrogen bonds       : angle       4.18931 (  969)
  link_BETA1-4         : bond        0.00564 (    5)
  link_BETA1-4         : angle       1.80787 (   15)
  link_NAG-ASN         : bond        0.00427 (   10)
  link_NAG-ASN         : angle       3.32444 (   30)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7521 (mt) cc_final: 0.7241 (mp)
REVERT: A  517 ASP cc_start: 0.8623 (t0) cc_final: 0.8407 (t0)
REVERT: A  747 MET cc_start: 0.8253 (mtp) cc_final: 0.7981 (mtp)
REVERT: A  894 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8288 (t80)
REVERT: A  955 ASP cc_start: 0.8576 (t0) cc_final: 0.8273 (t0)
REVERT: A  970 TYR cc_start: 0.8256 (m-80) cc_final: 0.7779 (m-80)
REVERT: A 1208 MET cc_start: 0.9160 (tpp) cc_final: 0.8939 (tpt)
REVERT: A 1252 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 83
  average time/residue: 0.0673
  time to fit residues: 8.3256
Evaluate side-chains
  83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  610 MET
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  789 SER
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1177 MET
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1252 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0470
   chunk 76 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.089201 restraints weight = 11700.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.60
r_work: 0.2933 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7714  Z= 0.099
  Angle     :  0.586   9.532  10553  Z= 0.264
  Chirality :  0.040   0.271   1274
  Planarity :  0.003   0.028   1272
  Dihedral  :  8.798 104.095   1621
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.38 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.29), residues: 912
  helix:  1.03 (0.25), residues: 501
  sheet: -0.61 (0.55), residues: 84
  loop : -1.43 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 693 
 TYR   0.009   0.001   TYR A 886 
 PHE   0.014   0.001   PHE A 791 
 TRP   0.010   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7694)
  covalent geometry    : angle       0.56209 (10498)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.63502 (   10)
  hydrogen bonds       : bond        0.03261 (  329)
  hydrogen bonds       : angle       4.01404 (  969)
  link_BETA1-4         : bond        0.00618 (    5)
  link_BETA1-4         : angle       1.64934 (   15)
  link_NAG-ASN         : bond        0.00556 (   10)
  link_NAG-ASN         : angle       2.96075 (   30)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7505 (mt) cc_final: 0.7229 (mp)
REVERT: A  894 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8187 (t80)
REVERT: A  970 TYR cc_start: 0.8239 (m-80) cc_final: 0.7872 (m-80)
REVERT: A 1252 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8450 (mp)
  outliers start: 12
  outliers final: 5
  residues processed: 76
  average time/residue: 0.0708
  time to fit residues: 7.8856
Evaluate side-chains
  72 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1252 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0470
   chunk 33 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.6878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.089622 restraints weight = 11767.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.61
r_work: 0.2946 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7714  Z= 0.098
  Angle     :  0.575   9.560  10553  Z= 0.262
  Chirality :  0.041   0.267   1274
  Planarity :  0.003   0.026   1272
  Dihedral  :  8.334 103.063   1621
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.76 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.29), residues: 912
  helix:  1.20 (0.25), residues: 500
  sheet: -0.62 (0.55), residues: 84
  loop : -1.34 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 619 
 TYR   0.009   0.001   TYR A 654 
 PHE   0.014   0.001   PHE A 791 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7694)
  covalent geometry    : angle       0.55248 (10498)
  SS BOND              : bond        0.00173 (    5)
  SS BOND              : angle       0.64247 (   10)
  hydrogen bonds       : bond        0.03176 (  329)
  hydrogen bonds       : angle       3.92123 (  969)
  link_BETA1-4         : bond        0.00558 (    5)
  link_BETA1-4         : angle       1.74316 (   15)
  link_NAG-ASN         : bond        0.00502 (   10)
  link_NAG-ASN         : angle       2.83327 (   30)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7495 (mt) cc_final: 0.7212 (mp)
REVERT: A  894 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8160 (t80)
REVERT: A  970 TYR cc_start: 0.8211 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  976 LYS cc_start: 0.7913 (tptm) cc_final: 0.7685 (tppt)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0711
  time to fit residues: 8.1826
Evaluate side-chains
  74 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1177 MET
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0570
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0670
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.6242

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.088092 restraints weight = 11931.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.63
r_work: 0.2920 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7714  Z= 0.130
  Angle     :  0.595   9.675  10553  Z= 0.271
  Chirality :  0.042   0.252   1274
  Planarity :  0.003   0.026   1272
  Dihedral  :  8.192 101.661   1621
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.28 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.29), residues: 912
  helix:  1.21 (0.25), residues: 500
  sheet: -0.60 (0.54), residues: 84
  loop : -1.33 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1241 
 TYR   0.008   0.001   TYR A 546 
 PHE   0.016   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7694)
  covalent geometry    : angle       0.57174 (10498)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       0.70357 (   10)
  hydrogen bonds       : bond        0.03445 (  329)
  hydrogen bonds       : angle       3.98508 (  969)
  link_BETA1-4         : bond        0.00567 (    5)
  link_BETA1-4         : angle       1.75955 (   15)
  link_NAG-ASN         : bond        0.00452 (   10)
  link_NAG-ASN         : angle       2.87048 (   30)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7451 (mt) cc_final: 0.7176 (mp)
REVERT: A  517 ASP cc_start: 0.8522 (t0) cc_final: 0.8312 (t0)
REVERT: A  894 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8233 (t80)
REVERT: A  970 TYR cc_start: 0.8204 (m-80) cc_final: 0.7812 (m-80)
REVERT: A  976 LYS cc_start: 0.7982 (tptm) cc_final: 0.7704 (tppt)
  outliers start: 13
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0708
  time to fit residues: 7.8027
Evaluate side-chains
  77 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue  996 ILE
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1177 MET
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0770
   chunk 78 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.7744

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.087778 restraints weight = 11789.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.61
r_work: 0.2914 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7714  Z= 0.137
  Angle     :  0.598   9.604  10553  Z= 0.274
  Chirality :  0.042   0.248   1274
  Planarity :  0.003   0.026   1272
  Dihedral  :  8.078 100.348   1621
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.40 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.29), residues: 912
  helix:  1.18 (0.25), residues: 500
  sheet: -0.61 (0.54), residues: 84
  loop : -1.27 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1241 
 TYR   0.008   0.001   TYR A 546 
 PHE   0.016   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7694)
  covalent geometry    : angle       0.57526 (10498)
  SS BOND              : bond        0.00251 (    5)
  SS BOND              : angle       0.70813 (   10)
  hydrogen bonds       : bond        0.03552 (  329)
  hydrogen bonds       : angle       3.97752 (  969)
  link_BETA1-4         : bond        0.00574 (    5)
  link_BETA1-4         : angle       1.71247 (   15)
  link_NAG-ASN         : bond        0.00448 (   10)
  link_NAG-ASN         : angle       2.89177 (   30)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7488 (mt) cc_final: 0.7212 (mp)
REVERT: A  894 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8379 (t80)
REVERT: A  970 TYR cc_start: 0.8196 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  976 LYS cc_start: 0.7987 (tptm) cc_final: 0.7729 (tppt)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0683
  time to fit residues: 8.2023
Evaluate side-chains
  80 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue  996 ILE
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.089504 restraints weight = 11790.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.61
r_work: 0.2939 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7714  Z= 0.104
  Angle     :  0.575   9.546  10553  Z= 0.264
  Chirality :  0.041   0.264   1274
  Planarity :  0.003   0.026   1272
  Dihedral  :  7.772  98.756   1621
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.28 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.29), residues: 912
  helix:  1.27 (0.25), residues: 500
  sheet: -0.56 (0.54), residues: 84
  loop : -1.30 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 619 
 TYR   0.008   0.001   TYR A 886 
 PHE   0.012   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.005   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7694)
  covalent geometry    : angle       0.55396 (10498)
  SS BOND              : bond        0.00188 (    5)
  SS BOND              : angle       0.62573 (   10)
  hydrogen bonds       : bond        0.03190 (  329)
  hydrogen bonds       : angle       3.94936 (  969)
  link_BETA1-4         : bond        0.00505 (    5)
  link_BETA1-4         : angle       1.56740 (   15)
  link_NAG-ASN         : bond        0.00492 (   10)
  link_NAG-ASN         : angle       2.73623 (   30)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.7450 (mt) cc_final: 0.7178 (mp)
REVERT: A  894 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (t80)
REVERT: A  970 TYR cc_start: 0.8192 (m-80) cc_final: 0.7792 (m-80)
REVERT: A  976 LYS cc_start: 0.7929 (tptm) cc_final: 0.7613 (tppt)
  outliers start: 11
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0516
  time to fit residues: 5.9582
Evaluate side-chains
  76 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  894 PHE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  927 ASN
Chi-restraints excluded: chain A residue  996 ILE
Chi-restraints excluded: chain A residue 1175 VAL
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 515 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.089122 restraints weight = 11828.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.61
r_work: 0.2934 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7714  Z= 0.114
  Angle     :  0.575   9.578  10553  Z= 0.264
  Chirality :  0.041   0.256   1274
  Planarity :  0.003   0.026   1272
  Dihedral  :  7.645  97.693   1621
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.28 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.29), residues: 912
  helix:  1.27 (0.25), residues: 500
  sheet:  0.01 (0.61), residues: 64
  loop : -1.33 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1136 
 TYR   0.008   0.001   TYR A 886 
 PHE   0.014   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A 960 
 HIS   0.004   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7694)
  covalent geometry    : angle       0.55440 (10498)
  SS BOND              : bond        0.00207 (    5)
  SS BOND              : angle       0.69907 (   10)
  hydrogen bonds       : bond        0.03319 (  329)
  hydrogen bonds       : angle       3.92757 (  969)
  link_BETA1-4         : bond        0.00495 (    5)
  link_BETA1-4         : angle       1.53999 (   15)
  link_NAG-ASN         : bond        0.00463 (   10)
  link_NAG-ASN         : angle       2.74289 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1931.28 seconds
wall clock time: 33 minutes 35.61 seconds (2015.61 seconds total)